I found that making non-specialized ships is ineffective. A warhammer 40k-esque cruiser with broadside cannons and forward lasers/ions is (while fun) kind of shitty on its own, at least early on. And by kind of shitty I mean you'll be killing plenty of ships, but the repairs will eat up almost all of your profits in most cases. You'll start fights by flying in and getting lasers off, turn broadside until your shields are down and cannons damaged, show them your other set of cannons, all the time taking massive hull and weapon damage.
Cannons by themselves are really powerful. I've had the most success by making a straight up hammerhead type ship with a massive row of forward cannons. Placing shields between your cannons means you need to stagger the rooms. 1 large with 2 small cannons on either side with a single shell factory worked well for me. even as cannons were destroyed my crew could still keep the rest operational because of door/factory placement. Biggest thing I struggled with was maneuverability. Cannons don't take a lot of energy, most of the crew are carrying shells. A few carrying batteries to thrusters. Placing more thrusters all over (especially on the sides of the forward cannons for swiveling) meant crew running the entire length of the ship, or making more room for reactors. It's a pain in the ass to modify blueprints in certain ways, as far as I know you can't copy/paste specific sections.
I bought a second ship and only equipped it with ion beams (about 7) spaced as closely together as I could while still being able to fit armor between them. Shields protecting the emitters close up, armor jutting out to intercept cannon fire. That setup took a shit ton of reactors and crew, and even with 2-wide corridors and plenty of extra crew I couldn't keep the beams firing full time. But still, that ship and the bomber made short work of almost everything and I never had to pay a lot for repairs. The enemy weapon systems would just get demolished by ion beams while my bomber punched through to key targets.
Remember you don't have to let crew roam the entire ship. You can cut off your engine room and attach two large crew quarters so that they're working engines full-time and not roaming the length of the ship. I think this is the best way to build medium and large ships. But losing specialized crew to unprotected hallways can end badly..
Use shield generators and battery storage rooms. They're worth it. In my experience glass cannon doesn't work. You'll kill the enemies but lose profit to repair costs. Shields save you money allowing for more upgrades.